The invention provides an attack-perceived multi-domain elastic optical network route and frequency spectrum distribution method and system. The method comprises the following steps: classifying services according to service paths when the services arrive so as to determine the services of the LRps type, the LRst type and the LRin type, wherein the LRps expresses passing through or ending at the domain, the LRst expresses starting from the domain, and the LRin expresses that a source node and a host node are in the domain; determining a candidate path set through a step; estimating an in-domain path of each candidate path by use of a safe estimation matrix aiming at each candidate in the candidate path set, thereby determining the path with the minimum entire security risk; distributing a transmission optical path for the service of each type based on the determined path; and distributing the frequency spectrum for the service on the selected transmission optical path based on the attack perception constraint. Through the adoption of the method and system provided by the invention, the possible security threat can be estimated so as to perform the route selection and frequency spectrum distribution according to the estimation result; therefore, the attach can be effectively perceived, and the physical layer security of the multi-domain elastic optical network is enhanced.